[gmx-users] RE: modelling a new molecule in OPLS

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jun 20 19:44:26 CEST 2008


Just to add my response on the pile (and do take the previous advice)
what you show here displays a problem of yours with respect to
molecular dynamics simulations. That naming should be consistent,
sure, if you know what you're doing you can sort of ignore warnings
like 'atom names don't match (ABC1 - 1ABC)'. But the warnings about
bond/angle/dihedral defaults and using zeroes. If one thinks to do
standard stuff and stumbles upon one of these, sure, we'll help, and
we did (check the archives). But if you're doing your own calculations
for a force field and then come up with this... Now working on a force
field, at least you should be natively aware that a bond definition
requires two atoms and a bond length (and possibly a force constant).
An angle is not created by simply listing three atoms. You need an
angle! Likewise for a dihedral. You should probably spend some (more)
time reading chapters 4 and 5 of the manual.



On Fri, Jun 20, 2008 at 3:53 PM, Vitaly Chaban <vvchaban at gmail.com> wrote:
>> I have built an all atom topology file for "chaps" as i have already
>> discussed in previous mails, with charges from Gaussian DFT. The current
>> problem is with the grompp.
> I think you should at least consult the existing examples of force
> fields.
> Also, everybody here will be very happy if you not send so lengthy messages to
> the list. There's no sense to cite all errors the programme displays.
> --
> Vitaly V. Chaban
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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